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- PDB-3gy4: A comparative study on the inhibition of bovine beta-trypsin by b... -

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Basic information

Entry
Database: PDB / ID: 3gy4
TitleA comparative study on the inhibition of bovine beta-trypsin by bis-benzamidines diminazene and pentamidine by X-ray crystallography and ITC
ComponentsCationic trypsin
KeywordsHYDROLASE / bovine beta-trypsin / p-amino benzamidine / protein-ligand complex / protein-ligand interaction / Calcium / Digestion / Disulfide bond / Metal-binding / Protease / Secreted / Serine protease / Zymogen
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
P-AMINO BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPerilo, C.S. / Pereira, M.T. / Santoro, M.M. / Nagem, R.A.P.
CitationJournal: Int.J.Biol.Macromol. / Year: 2010
Title: Structural binding evidence of the trypanocidal drugs Berenil and Pentacarinate active principles to a serine protease model.
Authors: Perilo, C.S. / Pereira, M.T. / Santoro, M.M. / Nagem, R.A.
History
DepositionApr 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,38714
Polymers23,3241
Non-polymers1,06313
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.265, 58.106, 66.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cationic trypsin / Beta-trypsin / Alpha-trypsin chain 1 / Alpha-trypsin chain 2


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pancreatic / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 378 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PBZ / P-AMINO BENZAMIDINE


Mass: 136.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG8000, 0.1M ammonium sulfate, 0.05M Tris-HCl, 0.008M CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 20, 2006
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. all: 31378 / Num. obs: 30624 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rsym value: 0.037 / Net I/σ(I): 29.21
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 8.9 / Num. unique all: 1991 / Rsym value: 0.122 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.138 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.078 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17539 1253 4.1 %RANDOM
Rwork0.15547 ---
obs0.15629 29342 97.7 %-
all-31303 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.858 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 61 365 2055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221771
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9752404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2352660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11815288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.621152
X-RAY DIFFRACTIONr_chiral_restr0.0790.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021285
X-RAY DIFFRACTIONr_nbd_refined0.2630.2910
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2274
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.243
X-RAY DIFFRACTIONr_mcbond_it0.6261.51147
X-RAY DIFFRACTIONr_mcangle_it0.95421818
X-RAY DIFFRACTIONr_scbond_it1.6453706
X-RAY DIFFRACTIONr_scangle_it2.4174.5577
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 80 -
Rwork0.235 2117 -
obs--97.17 %

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